While Mbappe did not get on the scoresheet in his final game for the Ligue 1 and Trophee des Champions winners, Ousmane Dembele and Fabian Ruiz both made the net bulge in the first half before Jake O'Brien pulled one back for Les Gones.
Despite their incredible revival in the top flight in the second half of the campaign, Pierre Sage's side could not prevent the capital giants from clinching their 15th Coupe de France honour, as Mbappe embarks on his new career path boasting an identical tally of 15 major honours from his time in Paris.
Inevitably, the former Monaco starlet - absent from PSG's Ligue 1 finale against Metz - returned to the starting lineup in his last game for the French champions, and the Real Madrid-bound attacker had two promising openings inside the first three minutes, but failed to convert either of them.
Lyon number two Lucas Perri was keeping Les Gones in the game in the earliest exchanges, but the Brazilian was at fault for PSG's opener in the 22nd minute, coming off his line and watching a Nuno Mendes cross sail over his head, giving Dembele the gift of an open net to head into.
PSG stave off second-half Lyon fightback
Enrique's rampant men thought that they had their second in the 24th minute, but Perri got the rub of the green this time after being fouled by Mbappe, who then wanted a penalty in the 34th minute as he took a tumble in the box.
However, while the 25-year-old was writhing in pain on the turf, Ruiz's header from a tight angle was blocked on the line by O'Brien, but the Spaniard forced the ball home through a few bodies at the second attempt to double Les Parisiens' lead.
While O'Brien's defensive efforts went unrewarded in that instance, the Irishman - who has been a goal threat from the back all season long - burst the final wide open in the 55th minute, meeting Rayan Cherki's set-piece with an exceptional header into the top corner.
PSG had not learned their aerial lessons and almost conceded the equaliser to another cross in the 63rd minute, but this time, Nicolas Tagliafico's header was too central to trouble Gianluigi Donnarumma.
The Italian would have been powerless to stop a goal-bound Alexandre Lacazette strike in the 76th minute, but Vitinha's deflection managed to turn the ball behind, and there were no further opportunities for Lyon to force an additional 30 minutes as PSG ended their three-year Coupe de France dry spell.